dont add new sequences to null groups!

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f78f958..8535d84 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -46,8 +46,6 @@ public class Alignment implements AlignmentI
    */\r
   public void addSequence(SequenceI snew) {\r
     sequences.addElement(snew);\r
-\r
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);\r
   }\r
 \r
   public void addSequence(SequenceI[] seq) {\r
@@ -389,6 +387,14 @@ public class Alignment implements AlignmentI
   {\r
     groups.clear();\r
     superGroup.clear();\r
+   int i=0;\r
+    while (i < sequences.size()) {\r
+     SequenceI s = getSequenceAt(i);\r
+     s.setColor(java.awt.Color.white);\r
+     i++;\r
+   }\r
+\r
+\r
   }\r
 \r
   /**    */\r
@@ -492,6 +498,17 @@ public class Alignment implements AlignmentI
   {\r
     return AAFrequency.calculate(sequences, 0, getWidth());\r
   }\r
+\r
+  public boolean isAligned()\r
+  {\r
+    int width = getWidth();\r
+    for (int i = 0; i < sequences.size(); i++)\r
+      if (getSequenceAt(i).getLength() != width)\r
+        return false;\r
+\r
+    return true;\r
+\r
+  }\r
 }\r
 \r
 \r